Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,508,789	A→T	9.4%	M109K (ATG→AAG)	PP_2203 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,508,789	0	A	T	9.4%	125.5 / 3.4	50	M109K (ATG→AAG)	PP_2203	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (28/16);  new base T (3/2);  total (32/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

GGCGGCACCAAAGGCGCTGAGAAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGTTGCTT  >  NC_002947/2508642‑2508934                                                                                                                                                    |                                                                                                                                                     ggcggcACCAAAGGCGCTGAGAAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCAt                                                                                                                                                     >  3:229487/1‑149 (MQ=255)         cAAAGGCGCTGAGAAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCa                                                                                                                                             <  1:344847/149‑1 (MQ=255)                gcTGAGAAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑g                                                                                                                                     >  2:129654/1‑149 (MQ=255)                    agaAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGccc                                                                                                                                 <  3:46909/149‑1 (MQ=255)                     gaAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCt                                                                                                                                >  2:380160/1‑149 (MQ=255)                                 cTAGGCTGAGCAGCAGTTGTTGGCGACCACGGTTGCCTGGCCATCCGTGGTCACCCCGATGCCCTGGTCGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGc                                                                                                                    <  8:351967/149‑1 (MQ=255)                                      cTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTg                                                                                                               <  8:193217/149‑1 (MQ=255)                                          gCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCc‑a                                                                                                          <  4:229487/149‑1 (MQ=255)                                              ctgtagtGGGCGACCCCGGTGCCCTGGCCATCCTGGGCCACCCCGATCACCTGGTAGGCAGCCTTGGGGCCACCCATCTCCCGGCCGGGCGACCCCTGGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCc‑agcag                                                                                                      <  8:186053/147‑1 (MQ=255)                                               agtagtTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAgg                                                                                                     >  2:31019/1‑149 (MQ=255)                                                     tGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCAcc                                                                                               >  7:101061/1‑149 (MQ=255)                                                       gCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCt                                                                                              <  7:84258/148‑1 (MQ=255)                                                         gACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCt                                                                                           >  7:126356/1‑149 (MQ=255)                                                                gtgtCCTGGCCATCCTGGGGCACCCCGATTACCTGGTAGGCATCCTTGTGGTCACCCATCGCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTcggccgg                                                                                    <  5:69966/149‑1 (MQ=255)                                                                     cgggCCATCCTGGGTCACCCGGATGACCGGGTCGGCATCGTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCTTGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCCGAGCAGGTGCGCCTGCtggc                                                                                        <  8:326437/139‑4 (MQ=255)                                                                     cTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCCGAGCAGGTGCGCCTGCtggc                                                                                        >  7:326437/1‑138 (MQ=255)                                                                      tGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTg                                                                              >  4:44830/1‑149 (MQ=255)                                                                            tCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGACCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTc                                                                        <  5:163199/149‑1 (MQ=255)                                                                              cTGGGTCAGCCTGATGACCTGGTTGGAATCGTTGTGGTCACCAATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCAGCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTcga                                                                      <  2:89666/149‑1 (MQ=255)                                                                                 ggTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTcgacg                                                                    <  6:377322/148‑1 (MQ=255)                                                                                     aCCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACtt                                                               >  5:160505/1‑149 (MQ=255)                                                                                      ccccGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTg                                                              >  3:18678/1‑149 (MQ=255)                                                                                       cccGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTgc                                                             >  8:165932/1‑149 (MQ=255)                                                                                       cccGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTgc                                                             >  1:292069/1‑149 (MQ=255)                                                                                       accGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTgc                                                             >  5:139019/2‑149 (MQ=255)                                                                                          gATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTgccgc                                                          >  2:345501/1‑149 (MQ=255)                                                                                              acgtGGTTGGAAGCCTTGTGGACCCCCATCTCCAGGCCGGGCGCGCCATTGGGCTTGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGa                                                       <  2:292069/145‑1 (MQ=255)                                                                                                   gTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGACGCCGATAA‑ccc                                                >  5:34340/1‑149 (MQ=255)                                                                                                      ggCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGACC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCgg                                             >  7:35706/1‑149 (MQ=255)                                                                                                       ccttCCTTGTTGACACCAATCTCTATTACGGGCGAGCCCATGGGCATGCCGGGCACCGCCA‑GGCGCTTGTGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCGCGTGGCCTTCGACGAACTTGCCGCCGTTCA‑CCCCGgt                                            <  6:102042/146‑1 (MQ=255)                                                                                                                  gTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCacgacg                                 <  7:165932/149‑1 (MQ=255)                                                                                                                       ccATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAgg                            >  5:323728/1‑149 (MQ=255)                                                                                                                            tcCATGCCGGGCGAGCCCATGGGCCTGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTCGCC‑AGCAGGCGCCCCTGCTCGGCCGGCACGTGGCCTTCGCCGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGCCGCAAGGCCTgg                       >  3:43240/1‑149 (MQ=255)                                                                                                                            tcCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTgg                       >  2:257704/1‑149 (MQ=255)                                                                                                                             ccATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgc                      >  1:21759/1‑149 (MQ=255)                                                                                                                             ccATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgc                      >  2:81163/1‑149 (MQ=255)                                                                                                                              cATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgcg                     >  4:257625/1‑149 (MQ=255)                                                                                                                               aTGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgcgc                    >  4:226368/1‑149 (MQ=255)                                                                                                                               aTGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgcgc                    >  1:200493/1‑149 (MQ=255)                                                                                                                                    gggcatgCCCATGGGCTCGCCCGGCACCGCCAGGGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCCCg                >  1:242249/7‑149 (MQ=255)                                                                                                                                      gCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGcc              >  5:137461/1‑148 (MQ=255)                                                                                                                                        gAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCACCCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGa            <  1:257704/149‑1 (MQ=255)                                                                                                                                           cccATGGGCTCGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGCTCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCCCGCCGAGGCg        >  7:352027/1‑149 (MQ=255)                                                                                                                                           cccATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCg        >  3:172168/1‑149 (MQ=255)                                                                                                                                            ccATGGGCTCGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgc                      >  4:99516/1‑134 (MQ=255)                                                                                                                                            ccATGGGCTCGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGgc                      <  3:99516/134‑1 (MQ=255)                                                                                                                                            ccATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGt       >  6:258633/1‑149 (MQ=255)                                                                                                                                                gcgCAGGCCCGCCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGGGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGTTGc    <  1:129654/146‑1 (MQ=255)                                                                                                                                                  gCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGTTGCtt  >  3:165972/1‑148 (MQ=255)                                                                                                                                                  gCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGTTGCtt  >  1:315058/1‑148 (MQ=255)                                                                                                                                                    |                                                                                                                                                     GGCGGCACCAAAGGCGCTGAGAAACAGCGCCCCTAGGCTGAGCATCAGTAGTTGGCGACCACGGTGTCCTGGCCATCCTGGGTCACCCCGATGACCTGGTAGGCATCCTTGTGGTCACCCATCTCCATGCCGGGCGAGCCCATGGGCATGCCCGGCACCGCCA‑GGCCCTTGAGGTCGTTGCGTTTGGCC‑AGCAGGCGCACCTGCTCGGCCGGCACGTGGCCTTCGACGAACTTGCCGCCGATCA‑CCCCGGTGTGGCACGACGCAAGGCGTGGCGCCACGCCGAGGCGTTGCTT  >  NC_002947/2508642‑2508934

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑